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comparison tool_dependencies.xml @ 0:af7ff8187d09 draft

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author iuc
date Wed, 11 Dec 2013 08:46:27 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="snpEff" version="3.4">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_4_core.zip</action>
7 <action type="move_directory_files">
8 <source_directory>.</source_directory>
9 <destination_directory>$INSTALL_DIR</destination_directory>
10 </action>
11 <action type="set_environment">
12 <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
13 </action>
14 <action type="set_environment">
15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
16 </action>
17 </actions>
18 </install>
19 <readme>
20
21 SnpEff and SnpSift ( http://snpeff.sourceforge.net/ )
22
23 SnpEff is a variant annotation and effect prediction tool by Pablo Cingolani.
24 It annotates and predicts the effects of variants on genes (such as amino acid changes).
25
26 This repository contains a tool_dependencies.xml file that downloads and installs SnpEff and SnpSift (SnpEff.jar and SnpSift.jar)
27
28 The install create an environment variable: SNPEFF_JAR_PATH that contains the path to the jar files. Tools using this can generate a command line:
29 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config ...
30
31 The snpEff.config file is also installed, which specifies the default location for installed SnpEff genome databases:
32 data_dir = ~/snpEff/data/
33
34 The location of a genome database can be set via the commandline option -dataDir. Tools using this can generate a command line:
35 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir path_to_data_directory snpeff_database_name input.vcf
36
37 Another way to change the location of data_dir would be to create a symbolic link in the galaxy HOME directory:
38 ln -s genome_data_path/snpEff ~/snpEff
39
40 SnpEff citation:
41 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
42
43 SnpSift citation:
44 "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
45
46
47 </readme>
48 </package>
49 </tool_dependency>
50